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Inventors have long been making the case that patents spur innovation by encouraging inventors to publicly disclose their creations and share their knowledge. So why is industry so cautious about welcoming the proposed unified patent system in the EU, which … Read more >

The saying that “life sciences is like a puzzle” has never been more true than it is today. The life sciences are in the midst of a dramatic transformation as technology redefines what is possible for human health and healthcare. That’s why the upcoming Bio-IT World event in Boston, April 21-23, holds so much promise for moving the conversation forward and sharing knowledge that truly helps people.

As the show approaches, we’re excited to roll out a new resource for you that offers an optimized compendium of codes with benchmarks and replication recipes. When used on Intel®-based computing platforms, and in concert with other Intel® software tools and products, such as Intel® Solid-State Drives (Intel® SSDs), the optimized code can help you decipher data and accelerate the path to discovery.

Industry leaders and authors of key genomic codes have supported this new resource to ensure that genome processing runs as fast as possible on Intel® based systems and clusters. The results have been significantly improved speed of key genomic programs and the development of new hardware and system solutions to get genome sequencing and processing down to minutes instead of days.

Download codes

If you’re looking for new tools to help handle growing molecular dynamics packages, which can span from hundreds to millions of particles, take advantage of these codes that are compatible with both Intel® Xeon® processors and Intel® Xeon® Phi™ coprocessors and allow you to “reuse” rather than “recode:”

AMBER 14

GROMACS 5.0 RC1

NAMD

LAMMPS

Quantum ESPRESSO

NWChem

Solve the cube

Finally, because life sciences is like a puzzle, look for a little fun and games at Bio-IT World that will test your puzzle solving skills and benefit charity.

If you’ll be at the show, be sure to grab a customized, genomic-themed Rubik’s Cube at the keynote session on Thursday, April 23, and join the fun trying to solve the puzzle after the speeches at our location on the show floor. Just by participating you will be eligible to win great prizes like a tablet, a Basis watch, or SMS headphones. Here’s a little Rubik’s Cube insight if you need help.

Plus, we’re giving away up to $10,000 to the Translational Genomics Research Institute (TGEN) in a tweet campaign that you can support. Watch for more details.

What questions do you have? We’re looking forward to seeing you at Bio-IT World next month.

Additionally we have updates in operating system and driver support and therefore a refresh to the previous posts on SSDs for Oracle is warranted to help you get the best out of the Intel SSD DC P3700 series for Oracle redo.

NVMe

One significant difference in the new SSDs is the change in interface and driver from AHCI and SATA to NVMe (Non-volatile memory express). For an introduction to NVMe see this video by James Myers and to understand the efficiency that NVMe brings read this post by Christian Black. As James noted, high performance, consistent, low latency Oracle redo logging also needs high endurance, therefore the P3700 is the drive to use. With a new interface comes a new driver, which fortunately is included in the Linux kernel at the Oracle supported Linux releases of Red Hat and Oracle Linux 6.5, 6.6 and 7.

I am using Oracle Linux 7.

Booting my system with both a RAID array of Intel SSD DC S3700 series and Intel SSD DC P3700 series shows two new disk devices:

As Oracle introduced support for 4KB sector sizes at Oracle release 11g R2, it is important to be at a minimum of this release for Oracle 12c to take full advantage of SSD for Oracle redo. However ‘out of the box’ as shown the P3700 presents a 512 byte sector size. We can use this ‘as is’ and set the Oracle parameter ‘disk_sector_size_override’ to true. With this we can then specify the blocksize to be 4KB when creating a redo log file. Oracle will then use 4KB redo log blocks and performance will not be compromised.

As a second option, the P3700 offers a feature called ‘Variable Sector Size’. Because we know we need 4KB sectors, we can set up the P3700 to present a 4KB sector size instead. This can then be used transparently by Oracle without the requirement for additional parameters. It is important to do this before you have configured or started to use the drive for Oracle as the operation is destructive of any existing data on the device.

A reboot is necessary because I am on Oracle Linux 7 with a UEK kernel at 3.8.13-35.3.1 and the NVMe needs to reset on the device. At Linux kernels 3.10 and above you can also run the following command with the system online to do the reset.

echo 1 > /sys/class/misc/nvme0/device/reset

The disk should now present the 4KB sector size we want for Oracle redo.

I then use udev to set the device permissions. Note: the scsi_id command can be run independently to find the device id to put in the file and the udevadm command used to apply the rules. Rebooting the system is useful during configuration to ensure that the correct permissions are applied on boot.

In previous posts I noted Oracle bug “16870214 : DB STARTUP FAILS WITH ORA-17510 IF SPFILE IS IN 4K SECTOR SIZE DISKGROUP” and even with Oracle 12.1.0.2 this bug is still with us. As both of my diskgroups have a 4KB sector size, this will affect me if I try to create a database in either without having applied patch 16870214.

With this bug, upon creating a database with DBCA you will see the following error.

The database is created and the spfile does exist so can be extracted as follows:

Running an OLTP workload with Oracle Redo on Intel® SSD DC P3700 series

To put the Oracle redo on P3700 through its paces I used a HammerDB workload. The redo is set with a standard production type configuration without commit_write and commit_wait parameters. A test shows we are running almost 100,000 transactions per second at redo over 500MB / second and therefore we would be archiving almost 2 TBs per hour.

Per Second

Per Transaction

Per Exec

Per Call

Redo size (bytes):

504,694,043.7

5,350.6

Log file sync even at this level of throughput is just above 1ms

Event

Waits

Total Wait Time (sec)

Wait Avg(ms)

% DB time

Wait Class

DB CPU

35.4K

59.1

log file sync

19,927,449

23.2K

1.16

38.7

Commit

…and the average log file parallel write showing the average disk response time to just 0.13ms

Event

Waits

%Time -outs

Total Wait Time (s)

Avg wait (ms)

Waits /txn

% bg time

log file parallel write

3,359,023

0

442

0.13

0.12

2237277.09

There are six log writers on this system. As with previous blog posts on SSDs I observed the log activity to be heaviest on the first three and therefore traced the log file parallel write activity on the first one with the following method:

The trace file shows the following results for log file parallel write latency to the P3700.

Log Writer Worker

Over 1ms

Over 10ms

Over 20ms

Max Elapsed

LG00

1.04%

0.01%

0.00%

14.83ms

Looking at a scatter plot of all of the log file parallel write latencies recorded in microseconds on the y axis clearly illustrate that any outliers are statistically insignificant and none exceed 15 milliseconds. Most of the writes are sub-millisecond on a system that is processing many millions of transactions a minute while doing so.

A subset of iostat data shows the the device is also far from full utilization.

As a confirmed believer in SSDs, I have long been convinced that most experiences of poor Oracle redo performance on SSDs has been due to an error in configuration such as sector size, block size and/or alignment as opposed to performance of the underlying device itself. In following the configuration steps I have outlined here, the Intel SSD DC P3700 series shows as an ideal candidate to take Oracle redo to the next level of performance without compromising endurance.

The most recent SDK for the Intel® RealSense™ F200 camera now includes 3D scanning. This is an amazing feature and will allow developers and digital artists to scan in real world objects to use in… Read more >

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We regularly update the Mesh Agent with many new features, but this week Bryan Roe had quite an impact with a complete suite of new features that are being rolled out in Mesh Agent v193. For people… Read more >

Mobility is expected to be a hot topic once again at HIMSS 2015 in Chicago. Tablets like the Surface and Windows-based versions of electronic health records (EHRs) from companies such as Allscripts are helping clinicians provide better care and be more efficient with their daily workflows.

The above video shows how the Surface and Allscripts’ Wand application are helping one cardiologist improve patient engagement while allowing more appointments throughout the day. You can read more in this blog.

Watch the video and let us know what questions you have. How are you leveraging mobile technology in your facility?

In November 2014, I led a session at SC14 (the event formerly known as “Supercomputing”) titled “The Future of Fortran”. I invited representatives from other vendors and members of the Fortran… Read more >

While GraphX provides nice abstractions and dataflow optimizations for parallel graph processing on top of Apache Spark*, there are still many challenges in applying it to an Internet-scale,… Read more >

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I’m participating in an IoT panel discussion on April 7 hosted by Intel. You can see details here. I’m am particularly looking forward to bringing a data center perspective to the discussion. There is a tendency when discussing the Internet of … Read more >

By Lisa Malloy, director of Policy Communications and Government Relations at Intel Next week, America’s most innovative companies will enter a lottery to keep some of the world’s brightest engineers, scientists and programmers employed here in the United States. Many … Read more >